https://github.com/satijalab/seurat
Tip revision: ff03fdf21f1b8fea9ee247d0fd83df5811507027 authored by AustinHartman on 05 December 2022, 22:48:27 UTC
Merge branch 'master' into release/4.3.0
Merge branch 'master' into release/4.3.0
Tip revision: ff03fdf
Seurat-package.Rd
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/zzz.R
\docType{package}
\name{Seurat-package}
\alias{Seurat}
\alias{Seurat-package}
\title{Seurat: Tools for Single Cell Genomics}
\description{
A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) \doi{10.1038/nbt.3192}, Macosko E, Basu A, Satija R, et al (2015) \doi{10.1016/j.cell.2015.05.002}, Stuart T, Butler A, et al (2019) \doi{10.1016/j.cell.2019.05.031}, and Hao, Hao, et al (2020) \doi{10.1101/2020.10.12.335331} for more details.
}
\section{Package options}{
Seurat uses the following [options()] to configure behaviour:
\describe{
\item{\code{Seurat.memsafe}}{global option to call gc() after many operations.
This can be helpful in cleaning up the memory status of the R session and
prevent use of swap space. However, it does add to the computational overhead
and setting to FALSE can speed things up if you're working in an environment
where RAM availability is not a concern.}
\item{\code{Seurat.warn.umap.uwot}}{Show warning about the default backend
for \code{\link{RunUMAP}} changing from Python UMAP via reticulate to UWOT}
\item{\code{Seurat.checkdots}}{For functions that have ... as a parameter,
this controls the behavior when an item isn't used. Can be one of warn,
stop, or silent.}
\item{\code{Seurat.limma.wilcox.msg}}{{Show message about more efficient
Wilcoxon Rank Sum test available via the limma package}}
\item{\code{Seurat.Rfast2.msg}}{{Show message about more efficient
Moran's I function available via the Rfast2 package}}
\item{\code{Seurat.warn.vlnplot.split}}{Show message about changes to
default behavior of split/multi violin plots}
}
}
\seealso{
Useful links:
\itemize{
\item \url{https://satijalab.org/seurat}
\item \url{https://github.com/satijalab/seurat}
\item Report bugs at \url{https://github.com/satijalab/seurat/issues}
}
}
\author{
\strong{Maintainer}: Paul Hoffman \email{seurat@nygenome.org} (\href{https://orcid.org/0000-0002-7693-8957}{ORCID})
Other contributors:
\itemize{
\item Andrew Butler \email{abutler@nygenome.org} (\href{https://orcid.org/0000-0003-3608-0463}{ORCID}) [contributor]
\item Saket Choudhary \email{schoudhary@nygenome.org} (\href{https://orcid.org/0000-0001-5202-7633}{ORCID}) [contributor]
\item Charlotte Darby \email{cdarby@nygenome.org} (\href{https://orcid.org/0000-0003-2195-5300}{ORCID}) [contributor]
\item Jeff Farrell \email{jfarrell@g.harvard.edu} [contributor]
\item Christoph Hafemeister \email{chafemeister@nygenome.org} (\href{https://orcid.org/0000-0001-6365-8254}{ORCID}) [contributor]
\item Yuhan Hao \email{yhao@nygenome.org} (\href{https://orcid.org/0000-0002-1810-0822}{ORCID}) [contributor]
\item Jaison Jain \email{jjain@nygenome.org} (\href{https://orcid.org/0000-0002-9478-5018}{ORCID}) [contributor]
\item Efthymia Papalexi \email{epapalexi@nygenome.org} (\href{https://orcid.org/0000-0001-5898-694X}{ORCID}) [contributor]
\item Patrick Roelli \email{proelli@nygenome.org} [contributor]
\item Rahul Satija \email{rsatija@nygenome.org} (\href{https://orcid.org/0000-0001-9448-8833}{ORCID}) [contributor]
\item Karthik Shekhar \email{kshekhar@berkeley.edu} [contributor]
\item Avi Srivastava \email{asrivastava@nygenome.org} (\href{https://orcid.org/0000-0001-9798-2079}{ORCID}) [contributor]
\item Tim Stuart \email{tstuart@nygenome.org} (\href{https://orcid.org/0000-0002-3044-0897}{ORCID}) [contributor]
\item Kristof Torkenczy (\href{https://orcid.org/0000-0002-4869-7957}{ORCID}) [contributor]
\item Shiwei Zheng \email{szheng@nygenome.org} (\href{https://orcid.org/0000-0001-6682-6743}{ORCID}) [contributor]
\item Satija Lab and Collaborators [funder]
}
}